PhenoSeq statistics

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Citations per year

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Popular tool citations

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Tool usage distribution map

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Associated diseases

Associated diseases

PhenoSeq specifications

Information


Unique identifier OMICS_12142
Name PhenoSeq
Interface Web user interface
Restrictions to use None
Input data Unaligned sequence(s) containing the V3 region
Input format FASTA
Computer skills Basic
Stability Stable
Maintained Yes

Taxon


  • Primates
    • Homo sapiens
  • Viruses
    • Human immunodeficiency virus 1
    • Human immunodeficiency virus 2

Maintainer


  • person_outline Paul Gorry <>

Publication for PhenoSeq

PhenoSeq in publications

 (11)
PMCID: 5799384
PMID: 29403064
DOI: 10.1038/s41598-018-20814-2

[…] all the machine-learning gtt tools have been developed primarily for hiv-1b and are now applied also with newly available v3-sequences of non-b subtype hiv-1. more recently a gtt tool called phenoseq was developed, which claims to be reliably predictive for the tropism of hiv-1 subtypes a, b, c, d, 01_ae and 02_ag., several guidelines have recommended pre-therapy gtt for patients […]

PMCID: 5571954
PMID: 28841646
DOI: 10.1371/journal.pone.0182384

[…] from 420 treatment-naïve hiv-1c infected ethiopians recruited 2009–2011. the v3 region was sequenced and the coreceptor usage was predicted by five tools: geno2pheno clinical–and clonal–models, phenoseq-c, c-pssm and raymond’s algorithm. the impact of baseline tropism on antiretroviral treatment (art) outcome was evaluated., of 352 patients with successful baseline v3 sequences, […]

PMCID: 5399036
PMID: 28484447
DOI: 10.3389/fimmu.2017.00376

[…] sample size, as these proviruses were functional at the time of entry. hiv-1 coreceptor usage was predicted using geno2pheno[coreceptor] (g2p) (), web pssm (both x4r5 and sinsi matrices) (), and phenoseq-b ()., patient envelope sequences were cloned into expression plasmid psviii-env by overlap extension pcr. in the first round pcr, the 1.2 kb v1–v5 fragment was amplified from the sequencing […]

PMCID: 5310022
PMID: 28196510
DOI: 10.1186/s12985-017-0703-y

[…] sequences generated by the ncbi’s translate tool were applied to the hivalign and the n-glycosite tool within the los alamos database. viral tropism was assessed using geno2pheno (g2p), webpssm and phenoseq platforms as well as using raymond’s and esbjörnsson’s rules. chi square test was used to determine independent variables association and anova applied on scale variables., at respective […]

PMCID: 5219668
PMID: 28061826
DOI: 10.1186/s12879-016-2163-1

[…] either positions 11 and 25 of the v3 loop are positively charged []. more sophisticated models have been developed that outperform the 11/25 rule, e.g. position specific scoring matrix (pssm) [] and phenoseq []. the most widely used geno2pheno and pssm tools are highly concordant (>85%) []. in our study the geno2pheno tools were chosen as the european guidelines recommend its use []. […]


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PhenoSeq institution(s)
Center for Virology, Burnet Institute, Melbourne, Australia

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